Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009016.1 Corchorus olitorius cultivar O-4 contig09044, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2664
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33


Found at i:1553 original size:21 final size:21

Alignment explanation


    Indices: 1527--1567  Score: 82
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1517 AAGGAAGAAA

                                 
       1527 TTTCAAGCTCATCGGAGTTGG
          1 TTTCAAGCTCATCGGAGTTGG

                                
       1548 TTTCAAGCTCATCGGAGTTG
          1 TTTCAAGCTCATCGGAGTTG

       1568 CCTAAGATGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34


Consensus pattern (21 bp):   
TTTCAAGCTCATCGGAGTTGG

Found at i:2644 original size:154 final size:154

Alignment explanation


    Indices: 2364--2664  Score: 460
    Period size: 154  Copynumber: 2.0  Consensus size: 154

       2354 ATTCGTATCA

                                                   *                         
       2364 ATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
          1 ATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCT

                            **                *                 *           *
       2429 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTGGATTTGGCAAACCTCAATGCTTTTCTTTCC
         66 ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-A

                                     
       2494 A-TTGTTTATGGACTAACTATAATC
        130 AGTTGTTTATGGACTAACTATAATC

                  *           *   *       *                                  
       2518 ATTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCT
          1 ATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCT

                 *                      *                         *          
       2583 ATCGGTGCCCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAAAGTTTTTCTTTAA
         66 ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTAA

                       *     
       2648 GTTGTTTATGGCCTAAC
        131 GTTGTTTATGGACTAAC


Statistics
Matches: 132,  Mismatches: 14, Indels: 2
        0.89            0.09        0.01

Matches are distributed among these distances:
 153    1  0.01
 154  131  0.99

ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41


Consensus pattern (154 bp):   
ATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCT
ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTAA
GTTGTTTATGGACTAACTATAATC
Done.